GRSDB Help: Glossary

1. QGRS Definition
2. Search & Analysis
3. Workbench Help
4. Understanding G-Scores
5. Dealing with overlaps
6. Glossary

Term	Definition
G-Group	The set of G's that form a tetrad, the foundation for the G-quadruplex structure. There are four such groups in a quadruplex. Each group will be of the same size in a particular quadruplex, and in any case must contain at least two G's.
G-Score	Each QGRS is assigned a score based on a system which rewards an arrangement of 'G's that is likely to form a unimolecular quadruplex. For calculation of G-scores, the size and distribution of the gaps in the predicted QGRS is taken into consideration. Also, the larger the size of the G-groups, the higher the score. The computed G-scores are dependent on the user selected maximum QGRS length. The highest possible G-score, using the default maximum QGRS length of 30, is 105.
Gap or Loop	The part of a QGRS that lies between two G-groups. For example, in the QGRS, (GG)GTA(GG)C(GG)TGA(GG), the four G-groups are in parentheses, so the three gaps are GTA, C, TGA. Note: up to one gap may be of length zero.
GRS	General term for a G-Rich Sequence.
G-Quadruplex	A three dimensional structure consisting of tetrads of G's connected by Hoogsteen bonds. Each tetrad is formed by taking one G from each G-group. The size of the G-group determines the number of tetrads found in the quadruplex.
QGRS	GRS that have the potential to form G-Quadruplex. The pattern for a QGRS is four groups of G's connected by arbitrary bases between each group. There are two categories of QGRS that are referred to in GRSDB: (30,2) denotes all QGRS of length at most 30 nucleotides and having at least 2 G’s per G-group. (45,3) denotes all QGRS of length at most 45 and having at least 3 G’s per G-group.
Near RNA Processing Sites	A QGRS is defined to be near an RNA processing sites if it's starting position is within 120 nucleotides of the site. Exception: This distance is 200 nt upstream or downstream of a polyA signal
Non-overlapping QGRS	Two sequences are said to be non-overlapping if their positions in the nucleotide sequence do not overlap. The default action of GRSDB is to only display non-overlapping sequences (although the user can show all sequences if they choose).
Overlapping QGRS	Two QGRS are said to overlap if their positions in the nucleotide sequence overlap. Overlaps are eliminated by selecting for higher scoring sequence.